feature request: ignore duplicate-marked reads

[anoronh4]

this issue is to request ignoring dup reads as an option. gatk best practice is to keep all duplicates in the bam, and i have read from a few issues here and here that a deduplicated (not just marked duplicate) bam is best for msisensor msi. therefore, we have to run an extra step and use almost twice as much storage to run msisensor from a deduplicated bam. ignoring dup reads from marked bam would avoid the trouble while hopefully not adding to the run time of msisensor

[Beifang]

Sure. We will provide this option soon.